vcfR documentation

by
Brian J. Knaus and Niklaus J. Grünwald

This material is intended for a one hour class on managing variant call format (VCF) data generated by the genotyping-by-sequencing (GBS) method. This class was a part of GBS_Winter_2017 at Oregon State University. It is assumed that the audience understands the GBS method (i.e., how the data were generated) and has a familiarity with the R language.

Outline

The dataset we will be using consists of samples of Phytophthora rubi, P. syringae and P. plurivora that are all mapped to a P. rubi reference. We’ll see that the other species do not map well to the P. rubi genome. This will provide a good example for troubleshooting batch effects in datasets.


Copyright © 2017, 2018 Brian J. Knaus. All rights reserved.

USDA Agricultural Research Service, Horticultural Crops Research Lab.